In regards to their respective vessels, Seska's betrayal was obviously worse given that she defected to the enemy and helped said enemy take over the ship. However, I don't think either betrayal had any serious effect on the Federation in anyway.

Not necessarily...didn't Seska say something about how it would be to Voyager's advantage to form ties with the Kazon and all? While it's not explicitly brought up, I could see her thinking that if she couldn't get Voyager on good terms with the Kazon, she might at least be able to establish some positive Cardassian ties with the DQ if and when the AQ powers made contact.